Origin IGS: taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatgagagttcaagctgacaagatgtaggttcacagccctttgcactctcagtacaacaactgtagaaccacacttcaagaaatctgtactgatatttaaagatacgtttttcattgataatattagcaaaaaggttcgcacacgaattgtatgcgaacctttttcatattttttaggtgtatgtttta Mask Tandem Repeat Region ================================================ taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Find is-nt database================================================ Query_seq: PI0048:PI0049|PI0048:PI0049:conserved hypothetical protein:outer membrane receptor protein (iron transport):->->:48555..48744 190 taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0048:PI0049|PI0048:PI0049:conserved hypothetical protein:outer membrane receptor protein (iron transport):->->:48555..48744 190 taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0048:PI0049|PI0048:PI0049:conserved hypothetical protein:outer membrane receptor protein (iron transport):->->:48555..48744 190 taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 42 End: 188 ......................................... M R V R T F L L I L S M K N V S L N I S T D F L K C G S T V V V L R V Q R A V N L H L V S L N S H .. Protein_Len: 41 Strand: + Start: 68 End: 190 ................................................................... M I N E K R I F K Y Q Y R F L E V W F Y S C C T E S A K G C E P T S C Q L E L S L Protein_Len: 58 Strand: - Start: 2 End: 175 . F C V G L F Y S F P E C V I R T R V K K S I N D I F F T D K F I L V S K K F H P E V T T T S L T C L A T F R C R T M ............... taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 66 End: 95 .................................................................ATTTAAAGATACGTTTTTCATTGATAATAT............................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 62 HP_score: -6.3 Tail_Score: -3.35679 Start: 18 End: 68 Full_Region: AAACATACACCTAAA AAATATGAAAAAGGTTCGCATAC AATTC GTGTGCGAACCTTTTTGCTAATA TTATCAATGAAAAAC .................AAATATGAAAAAGGTTCGCATACAATTCGTGTGCGAACCTTTTTGCTAATA.......................................................................................................................... TransTerm Strand: + Conf: 89 HP_score: -13.9 Tail_Score: -2.81045 Start: 24 End: 63 Full_Region: ACACCTAAAAAATAT GAAAAAGGTTCGCATAC AATTC GTGTGCGAACCTTTTTGC TAATATTATCAATGA .......................GAAAAAGGTTCGCATACAATTCGTGTGCGAACCTTTTTGC............................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -11.6 Tail_Score: -5.04265 Start: 30 End: 56 Full_Region: taatattagcaaaaa ggttcgcacacg aat tgtatgcgaacc tttttcatatttttt .............................ggttcgcacacgaattgtatgcgaacc...................................................................................................................................... Find igs database================================================ Query_seq: PI0048:PI0049|PI0048:PI0049:conserved hypothetical protein:outer membrane receptor protein (iron transport):->->:48555..48744 190 taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: pint_PI0048_PI0049|conserved hypothetical protein:outer membrane receptor protein (iron transport)|POSITIVE:POSITIVE|[48555,48744]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta taaaacatacacctaaaaaatatgaaaaaggttcgcatacaattcgtgtgcgaacctttttgctaatattatcaatgaaaaacgtatctttaaatatcagtacagatttcttgaagtgtggttctacagttgttgtactgagagtgcaaagggctgtgaacctacatcttgtcagcttgaactctcatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACAUACACCUAAAAAAUAUGAAAAAGGUUCGCAUACAAUUCGUGUGCGAACCUUUUUGCUAAUAUUAUCAAUGAAAAACGUAUCUUUAAAUAUCAGUACAGAUUUCUUGAAGUGUGGUUCUACAGUUGUUGUACUGAGAGUGCAAAGGGCUGUGAACCUACAUCUUGUCAGCUUGAACUCUCAUUA ........................((((((((((((((((.....))))))))))))))))(((.(((...((((.((((...((((............))))...)))))))).(((((((((.((((((.((((((.....))))))..))))))))))).))))..))).))).............. (-52.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGAGAGUUCAAGCUGACAAGAUGUAGGUUCACAGCCCUUUGCACUCUCAGUACAACAACUGUAGAACCACACUUCAAGAAAUCUGUACUGAUAUUUAAAGAUACGUUUUUCAUUGAUAAUAUUAGCAAAAAGGUUCGCACACGAAUUGUAUGCGAACCUUUUUCAUAUUUUUUAGGUGUAUGUUUUA ...(((((((.(((((((....((.......)).))))...))).)))))))............((((((.((((((.(((((((.((..(((((((((((.((........)).))))..))))))).(((((((((((((.((.....)).))))))))))))))).)))))))))))))..)))))) (-48.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 341 176 131 56 11 pint:PI0814|5end_conserved_hypothetical_protein_752946..753176_POSITIVE 325 158 111 107 49 pint:PI0052|5end_hypothetical_protein_52312..52542_POSITIVE 322 160 112 95 39 pint:PI1573|5end_transcription-repair_coupling_factor_1496429..1496659_POSITIVE 310 167 127 190 142 pint:PI1185|5end_hypothetical_protein_1106076..1106306_POSITIVE 309 148 104 143 96 pint:PI1779|5end_16S_rRNA_processing_protein_1711335..1711565_POSITIVE 299 177 136 76 34 pint:PI0313|5end_conserved_hypothetical_protein_294833..295063_POSITIVE 297 179 131 187 128 pint:PI0363|5end_hypothetical_protein_332832..333062_POSITIVE 292 176 135 88 49 pint:PI0855|5end_hypothetical_protein_789094..789324_POSITIVE 290 190 143 213 167 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 288 180 131 94 40 pint:PI2119|5end_conserved_hypothetical_protein;_possible_cytochrome_B_subunit_2068031..2068261_POSITIVE 285 187 149 38 5 pint:PI2117|5end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066017..2066247_POSITIVE 283 178 136 166 132 pint:PI1443|5end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1364560..1364790_POSITIVE 282 159 115 189 134 pint:PI0522|5end_50S_ribosomal_protein_L19_479004..479234_POSITIVE 282 159 115 71 16 pint:PI0521|5end_hypothetical_protein_478886..479116_POSITIVE 280 158 111 178 138 pint:PI1736|5end_topoisomerase_IV,_subunit_A_1654254..1654484_POSITIVE 279 177 135 194 155 pint:PI1858|5end_conserved_hypothetical_protein_1804400..1804630_POSITIVE 276 159 112 190 131 pint:PI1276|5end_hypothetical_protein_1194266..1194496_POSITIVE 276 178 133 148 102 pint:PI0833|5end_conserved_hypothetical_protein_770059..770289_POSITIVE 275 158 127 169 127 pint:PI0898|5end_conserved_hypothetical_protein_828474..828704_POSITIVE 270 186 141 154 109 pint:PI0331|5end_hypothetical_protein_311656..311886_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 455 61 25 66 30 pint:PI0048|3end_conserved_hypothetical_protein_48494..48644_POSITIVE 313 179 135 131 86 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 309 148 104 127 80 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 299 177 136 131 89 pint:PI0311|3end_hypothetical_protein_294968..295118_POSITIVE 299 177 136 103 61 pint:PI0312|3end_hypothetical_protein_294940..295090_POSITIVE 296 176 132 106 52 pint:PI0512|3end_conserved_hypothetical_protein_471440..471590_POSITIVE 295 153 113 66 14 pint:PI0171|3end_hypothetical_protein_164085..164235_POSITIVE 285 145 102 123 76 pint:PI2161|3end_hypothetical_protein_2108751..2108901_POSITIVE 282 159 115 56 1 pint:PI0520|3end_hypothetical_protein_478951..479101_POSITIVE 279 177 135 110 71 pint:PI1857|3end_guanylate_kinase_1804396..1804546_POSITIVE 278 176 135 127 73 pint:PI2074|3end_conserved_hypothetical_protein_2034375..2034525_POSITIVE 276 159 112 151 92 pint:PI1275|3end_indole-3-glycerol_phosphate_synthase_1194307..1194457_POSITIVE 272 157 115 143 90 pint:PI0480|3end_preprotein_translocase,_SecY_subunit_442993..443143_POSITIVE 271 156 115 87 36 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 261 178 131 90 31 pint:PI0135|3end_internalin-related_protein_127257..127407_POSITIVE 260 65 28 121 73 pint:PI2092|3end_hypothetical_protein_2049406..2049556_POSITIVE 259 183 141 75 23 pint:PI1488|3end_hypothetical_protein_1407829..1407979_POSITIVE 252 158 116 81 34 pint:PI1487|3end_hypothetical_protein_1407940..1408090_POSITIVE 251 158 118 93 47 pint:PI1892|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_1835547..1835697_POSITIVE 250 177 131 140 102 pint:PI0998|3end_possible_flavin_reductase_domain_protein_923336..923486_POSITIVE